Mercurial > repos > iuc > schicexplorer_schicqualitycontrol

annotate scHicQualityControl.xml @ 2:f623007a57d1 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit d350f8e73ae518245a21f9720f8282f06eb9cc5d
author iuc
date Fri, 14 Apr 2023 14:09:31 +0000
parents e06c31798a26
children
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2
f623007a57d1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit d350f8e73ae518245a21f9720f8282f06eb9cc5d
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1 <tool id="schicexplorer_schicqualitycontrol" name="@BINARY@" version="@TOOL_VERSION@.1" profile="@PROFILE@">
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2 <description>quality control for single-cell Hi-C interaction matrices</description>
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3 <macros>
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4 <token name="@BINARY@">scHicQualityControl</token>
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5 <import>macros.xml</import>
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6 </macros>
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7 <expand macro="requirements" />
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8 <command detect_errors="exit_code"><![CDATA[
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f623007a57d1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit d350f8e73ae518245a21f9720f8282f06eb9cc5d
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9 ## https://github.com/open2c/cooler/issues/299
f623007a57d1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit d350f8e73ae518245a21f9720f8282f06eb9cc5d
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10 cp '$matrix_scooler' matrix.scooler &&
f623007a57d1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit d350f8e73ae518245a21f9720f8282f06eb9cc5d
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11
0
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12 @BINARY@
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13
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f623007a57d1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit d350f8e73ae518245a21f9720f8282f06eb9cc5d
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14 --matrix matrix.scooler
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15 #if $chromosomes:
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16 #set $chromosome = ' '.join([ '\'%s\'' % $chrom for $chrom in str($chromosomes).split(' ') ])
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17 --chromosomes $chromosome
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18 #end if
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19 --minimumReadCoverage $minimumReadCoverage
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20 --minimumDensity $minimumDensity
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21 --maximumRegionToConsider $maximumRegionToConsider
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22 #if $dpi:
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23 --dpi $dpi
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24 #end if
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25 --outFileNameDensity plot_density.$image_file_format
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26 --outFileNameReadCoverage plot_read_coverage.$image_file_format
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27 --outFileNameQCReport report.txt
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28 --outputScool filtered_matrices.scool
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30 --threads @THREADS@
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32 && mv plot_density.$image_file_format plot_density
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33 && mv plot_read_coverage.$image_file_format plot_read_coverage
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36 ]]></command>
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37 <inputs>
1
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38 <expand macro="matrix_scooler_macro"/>
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39 <param name="minimumReadCoverage" type="integer" value="1000000" label="Minimum read coverage" help='Remove all samples with a lower read coverage as this value.' />
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40 <param name="minimumDensity" type="float" value="0.001" label="Minimum density" help='Remove all samples with a lower density as this value.' />
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41 <param name="maximumRegionToConsider" type="integer" value="30000000" label="Maximum region to consider" help='To compute the density, consider only this genomic distance around the diagonal.' />
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42 <param name='chromosomes' type='text' label='List of chromosomes to consider' help='Please separate the chromosomes by space'/>
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43 <param name='dpi' type='integer' label='DPI for image' help='Change the default resolution of the plot.' optional='true'/>
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44 <param name="image_file_format" type="select" label="Image output format">
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45 <option value="png" selected="True">png</option>
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46 <option value="svg">svg</option>
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47 <option value="pdf">pdf</option>
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48 </param>
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49 </inputs>
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50 <outputs>
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51 <data name='output_plot_density' from_work_dir='plot_density' format='png' label='Density'>
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52 <change_format>
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53 <when input="image_file_format" value="svg" format="svg" />
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54 <when input="image_file_format" value="pdf" format="pdf" />
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55 </change_format>
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56 </data>
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57 <data name='output_plot_read_coverage' from_work_dir='plot_read_coverage' format='png' label='Read coverage'>
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58 <change_format>
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59 <when input="image_file_format" value="svg" format="svg" />
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60 <when input="image_file_format" value="pdf" format="pdf" />
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61 </change_format>
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62 </data>
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63 <data name="report" from_work_dir="report.txt" format="txt" label="${tool.name} on ${on_string}: QC report"/>
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64 <data name="outFileName" from_work_dir="filtered_matrices.scool" format="scool" label="${tool.name} on ${on_string}: Filtered matrices"/>
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65
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66 </outputs>
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67 <tests>
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68 <test>
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69 <param name='matrix_scooler' value='test_matrix.scool' />
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70 <param name='minimumReadCoverage' value='100000' />
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71 <param name='minimumDensity' value='0.001' />
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72 <param name='maximumRegionToConsider' value='30000000' />
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73 <param name="image_file_format" value="png" />
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74 <param name="dpi" value="300" />
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75 <output name="output_plot_density" file="scHicQualityControl/density.png" ftype="png" compare="sim_size" delta="35000"/>
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76 <output name="output_plot_read_coverage" file="scHicQualityControl/coverage.png" ftype="png" compare="sim_size" delta="35000"/>
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77 <output name="report" file="scHicQualityControl/qc_report.txt" ftype="txt" compare="sim_size" delta="35000"/>
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78 <output name="outFileName" ftype="scool">
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79 <assert_contents>
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80 <has_h5_keys keys='Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz, Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz/bins,
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81 Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz/bins/chrom, Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz/bins/end,
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82 Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz/bins/start, Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz/chroms,
e06c31798a26 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
iuc
parents: 0
diff changeset
83 Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz/chroms/length, Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz/chroms/name,
e06c31798a26 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
iuc
parents: 0
diff changeset
84 Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz/indexes, Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz/indexes/bin1_offset,
e06c31798a26 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
iuc
parents: 0
diff changeset
85 Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz/indexes/chrom_offset, Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz/pixels,
e06c31798a26 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
iuc
parents: 0
diff changeset
86 Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz/pixels/bin1_id, Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz/pixels/bin2_id,
e06c31798a26 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
iuc
parents: 0
diff changeset
87 Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz/pixels/count, Diploid_1_CGTACTAG_ACTGCATA_R1fastqgz, Diploid_1_CGTACTAG_ACTGCATA_R1fastqgz/bins,
e06c31798a26 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
iuc
parents: 0
diff changeset
88 Diploid_1_CGTACTAG_ACTGCATA_R1fastqgz/bins/chrom, Diploid_1_CGTACTAG_ACTGCATA_R1fastqgz/bins/end,
e06c31798a26 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
iuc
parents: 0
diff changeset
89 Diploid_1_CGTACTAG_ACTGCATA_R1fastqgz/bins/start, Diploid_1_CGTACTAG_ACTGCATA_R1fastqgz/chroms,
e06c31798a26 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
iuc
parents: 0
diff changeset
90 Diploid_1_CGTACTAG_ACTGCATA_R1fastqgz/chroms/length, Diploid_1_CGTACTAG_ACTGCATA_R1fastqgz/chroms/name,
e06c31798a26 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
iuc
parents: 0
diff changeset
91 Diploid_1_CGTACTAG_ACTGCATA_R1fastqgz/indexes, Diploid_1_CGTACTAG_ACTGCATA_R1fastqgz/indexes/bin1_offset,
e06c31798a26 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
iuc
parents: 0
diff changeset
92 Diploid_1_CGTACTAG_ACTGCATA_R1fastqgz/indexes/chrom_offset, Diploid_1_CGTACTAG_ACTGCATA_R1fastqgz/pixels,
e06c31798a26 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
iuc
parents: 0
diff changeset
93 Diploid_1_CGTACTAG_ACTGCATA_R1fastqgz/pixels/bin1_id, Diploid_1_CGTACTAG_ACTGCATA_R1fastqgz/pixels/bin2_id,
e06c31798a26 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
iuc
parents: 0
diff changeset
94 Diploid_1_CGTACTAG_ACTGCATA_R1fastqgz/pixels/count, Diploid_1_CGTACTAG_CTAAGCCT_R1fastqgz, Diploid_1_CGTACTAG_CTAAGCCT_R1fastqgz/bins,
e06c31798a26 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
iuc
parents: 0
diff changeset
95 Diploid_1_CGTACTAG_CTAAGCCT_R1fastqgz/bins/chrom, Diploid_1_CGTACTAG_CTAAGCCT_R1fastqgz/bins/end,
e06c31798a26 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
iuc
parents: 0
diff changeset
96 Diploid_1_CGTACTAG_CTAAGCCT_R1fastqgz/bins/start, Diploid_1_CGTACTAG_CTAAGCCT_R1fastqgz/chroms,
e06c31798a26 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
iuc
parents: 0
diff changeset
97 Diploid_1_CGTACTAG_CTAAGCCT_R1fastqgz/chroms/length, Diploid_1_CGTACTAG_CTAAGCCT_R1fastqgz/chroms/name,
e06c31798a26 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
iuc
parents: 0
diff changeset
98 Diploid_1_CGTACTAG_CTAAGCCT_R1fastqgz/indexes, Diploid_1_CGTACTAG_CTAAGCCT_R1fastqgz/indexes/bin1_offset,
e06c31798a26 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
iuc
parents: 0
diff changeset
99 Diploid_1_CGTACTAG_CTAAGCCT_R1fastqgz/indexes/chrom_offset, Diploid_1_CGTACTAG_CTAAGCCT_R1fastqgz/pixels,
e06c31798a26 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
iuc
parents: 0
diff changeset
100 Diploid_1_CGTACTAG_CTAAGCCT_R1fastqgz/pixels/bin1_id, Diploid_1_CGTACTAG_CTAAGCCT_R1fastqgz/pixels/bin2_id,
e06c31798a26 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
iuc
parents: 0
diff changeset
101 Diploid_1_CGTACTAG_CTAAGCCT_R1fastqgz/pixels/count, Diploid_1_CGTACTAG_CTCTCTAT_R1fastqgz, Diploid_1_CGTACTAG_CTCTCTAT_R1fastqgz/bins,
e06c31798a26 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
iuc
parents: 0
diff changeset
102 Diploid_1_CGTACTAG_CTCTCTAT_R1fastqgz/bins/chrom, Diploid_1_CGTACTAG_CTCTCTAT_R1fastqgz/bins/end,
e06c31798a26 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
iuc
parents: 0
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103 Diploid_1_CGTACTAG_CTCTCTAT_R1fastqgz/bins/start, Diploid_1_CGTACTAG_CTCTCTAT_R1fastqgz/chroms,
e06c31798a26 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
iuc
parents: 0
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104 Diploid_1_CGTACTAG_CTCTCTAT_R1fastqgz/chroms/length, Diploid_1_CGTACTAG_CTCTCTAT_R1fastqgz/chroms/name,
e06c31798a26 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
iuc
parents: 0
diff changeset
105 Diploid_1_CGTACTAG_CTCTCTAT_R1fastqgz/indexes, Diploid_1_CGTACTAG_CTCTCTAT_R1fastqgz/indexes/bin1_offset,
e06c31798a26 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
iuc
parents: 0
diff changeset
106 Diploid_1_CGTACTAG_CTCTCTAT_R1fastqgz/indexes/chrom_offset, Diploid_1_CGTACTAG_CTCTCTAT_R1fastqgz/pixels,
e06c31798a26 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
iuc
parents: 0
diff changeset
107 Diploid_1_CGTACTAG_CTCTCTAT_R1fastqgz/pixels/bin1_id, Diploid_1_CGTACTAG_CTCTCTAT_R1fastqgz/pixels/bin2_id,
e06c31798a26 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
iuc
parents: 0
diff changeset
108 Diploid_1_CGTACTAG_CTCTCTAT_R1fastqgz/pixels/count, Diploid_1_CGTACTAG_GTAAGGAG_R1fastqgz, Diploid_1_CGTACTAG_GTAAGGAG_R1fastqgz/bins,
e06c31798a26 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
iuc
parents: 0
diff changeset
109 Diploid_1_CGTACTAG_GTAAGGAG_R1fastqgz/bins/chrom, Diploid_1_CGTACTAG_GTAAGGAG_R1fastqgz/bins/end,
e06c31798a26 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
iuc
parents: 0
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110 Diploid_1_CGTACTAG_GTAAGGAG_R1fastqgz/bins/start, Diploid_1_CGTACTAG_GTAAGGAG_R1fastqgz/chroms,
e06c31798a26 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
iuc
parents: 0
diff changeset
111 Diploid_1_CGTACTAG_GTAAGGAG_R1fastqgz/chroms/length, Diploid_1_CGTACTAG_GTAAGGAG_R1fastqgz/chroms/name,
e06c31798a26 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
iuc
parents: 0
diff changeset
112 Diploid_1_CGTACTAG_GTAAGGAG_R1fastqgz/indexes, Diploid_1_CGTACTAG_GTAAGGAG_R1fastqgz/indexes/bin1_offset,
e06c31798a26 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
iuc
parents: 0
diff changeset
113 Diploid_1_CGTACTAG_GTAAGGAG_R1fastqgz/indexes/chrom_offset, Diploid_1_CGTACTAG_GTAAGGAG_R1fastqgz/pixels,
e06c31798a26 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
iuc
parents: 0
diff changeset
114 Diploid_1_CGTACTAG_GTAAGGAG_R1fastqgz/pixels/bin1_id, Diploid_1_CGTACTAG_GTAAGGAG_R1fastqgz/pixels/bin2_id,
e06c31798a26 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
iuc
parents: 0
diff changeset
115 Diploid_1_CGTACTAG_GTAAGGAG_R1fastqgz/pixels/count, Diploid_1_CGTACTAG_TCTCTCCG_R1fastqgz,
e06c31798a26 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
iuc
parents: 0
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116 Diploid_1_CGTACTAG_TCTCTCCG_R1fastqgz/bins, Diploid_1_CGTACTAG_TCTCTCCG_R1fastqgz/bins/chrom,
e06c31798a26 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
iuc
parents: 0
diff changeset
117 Diploid_1_CGTACTAG_TCTCTCCG_R1fastqgz/bins/end, Diploid_1_CGTACTAG_TCTCTCCG_R1fastqgz/bins/start,
e06c31798a26 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
iuc
parents: 0
diff changeset
118 Diploid_1_CGTACTAG_TCTCTCCG_R1fastqgz/chroms, Diploid_1_CGTACTAG_TCTCTCCG_R1fastqgz/chroms/length,
e06c31798a26 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
iuc
parents: 0
diff changeset
119 Diploid_1_CGTACTAG_TCTCTCCG_R1fastqgz/chroms/name, Diploid_1_CGTACTAG_TCTCTCCG_R1fastqgz/indexes,
e06c31798a26 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
iuc
parents: 0
diff changeset
120 Diploid_1_CGTACTAG_TCTCTCCG_R1fastqgz/indexes/bin1_offset, Diploid_1_CGTACTAG_TCTCTCCG_R1fastqgz/indexes/chrom_offset,
e06c31798a26 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
iuc
parents: 0
diff changeset
121 Diploid_1_CGTACTAG_TCTCTCCG_R1fastqgz/pixels, Diploid_1_CGTACTAG_TCTCTCCG_R1fastqgz/pixels/bin1_id,
e06c31798a26 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
iuc
parents: 0
diff changeset
122 Diploid_1_CGTACTAG_TCTCTCCG_R1fastqgz/pixels/bin2_id, Diploid_1_CGTACTAG_TCTCTCCG_R1fastqgz/pixels/count,
e06c31798a26 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
iuc
parents: 0
diff changeset
123 Diploid_1_TAAGGCGA_AAGGAGTA_R1fastqgz, Diploid_1_TAAGGCGA_AAGGAGTA_R1fastqgz/bins,
e06c31798a26 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
iuc
parents: 0
diff changeset
124 Diploid_1_TAAGGCGA_AAGGAGTA_R1fastqgz/bins/chrom, Diploid_1_TAAGGCGA_AAGGAGTA_R1fastqgz/bins/end,
e06c31798a26 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
iuc
parents: 0
diff changeset
125 Diploid_1_TAAGGCGA_AAGGAGTA_R1fastqgz/bins/start, Diploid_1_TAAGGCGA_AAGGAGTA_R1fastqgz/chroms,
e06c31798a26 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
iuc
parents: 0
diff changeset
126 Diploid_1_TAAGGCGA_AAGGAGTA_R1fastqgz/chroms/length, Diploid_1_TAAGGCGA_AAGGAGTA_R1fastqgz/chroms/name,
e06c31798a26 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
iuc
parents: 0
diff changeset
127 Diploid_1_TAAGGCGA_AAGGAGTA_R1fastqgz/indexes, Diploid_1_TAAGGCGA_AAGGAGTA_R1fastqgz/indexes/bin1_offset,
e06c31798a26 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
iuc
parents: 0
diff changeset
128 Diploid_1_TAAGGCGA_AAGGAGTA_R1fastqgz/indexes/chrom_offset, Diploid_1_TAAGGCGA_AAGGAGTA_R1fastqgz/pixels,
e06c31798a26 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
iuc
parents: 0
diff changeset
129 Diploid_1_TAAGGCGA_AAGGAGTA_R1fastqgz/pixels/bin1_id, Diploid_1_TAAGGCGA_AAGGAGTA_R1fastqgz/pixels/bin2_id,
e06c31798a26 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
iuc
parents: 0
diff changeset
130 Diploid_1_TAAGGCGA_AAGGAGTA_R1fastqgz/pixels/count, Diploid_1_TAAGGCGA_CTAAGCCT_R1fastqgz,
e06c31798a26 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
iuc
parents: 0
diff changeset
131 Diploid_1_TAAGGCGA_CTAAGCCT_R1fastqgz/bins, Diploid_1_TAAGGCGA_CTAAGCCT_R1fastqgz/bins/chrom,
e06c31798a26 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
iuc
parents: 0
diff changeset
132 Diploid_1_TAAGGCGA_CTAAGCCT_R1fastqgz/bins/end, Diploid_1_TAAGGCGA_CTAAGCCT_R1fastqgz/bins/start,
e06c31798a26 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
iuc
parents: 0
diff changeset
133 Diploid_1_TAAGGCGA_CTAAGCCT_R1fastqgz/chroms, Diploid_1_TAAGGCGA_CTAAGCCT_R1fastqgz/chroms/length,
e06c31798a26 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
iuc
parents: 0
diff changeset
134 Diploid_1_TAAGGCGA_CTAAGCCT_R1fastqgz/chroms/name, Diploid_1_TAAGGCGA_CTAAGCCT_R1fastqgz/indexes,
e06c31798a26 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
iuc
parents: 0
diff changeset
135 Diploid_1_TAAGGCGA_CTAAGCCT_R1fastqgz/indexes/bin1_offset, Diploid_1_TAAGGCGA_CTAAGCCT_R1fastqgz/indexes/chrom_offset,
e06c31798a26 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
iuc
parents: 0
diff changeset
136 Diploid_1_TAAGGCGA_CTAAGCCT_R1fastqgz/pixels, Diploid_1_TAAGGCGA_CTAAGCCT_R1fastqgz/pixels/bin1_id,
e06c31798a26 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
iuc
parents: 0
diff changeset
137 Diploid_1_TAAGGCGA_CTAAGCCT_R1fastqgz/pixels/bin2_id, Diploid_1_TAAGGCGA_CTAAGCCT_R1fastqgz/pixels/count,
e06c31798a26 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
iuc
parents: 0
diff changeset
138 Diploid_2_AAGAGGCA_CGTCTAAT_R1fastqgz, Diploid_2_AAGAGGCA_CGTCTAAT_R1fastqgz/bins,
e06c31798a26 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
iuc
parents: 0
diff changeset
139 Diploid_2_AAGAGGCA_CGTCTAAT_R1fastqgz/bins/chrom, Diploid_2_AAGAGGCA_CGTCTAAT_R1fastqgz/bins/end,
e06c31798a26 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
iuc
parents: 0
diff changeset
140 Diploid_2_AAGAGGCA_CGTCTAAT_R1fastqgz/bins/start, Diploid_2_AAGAGGCA_CGTCTAAT_R1fastqgz/chroms,
e06c31798a26 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
iuc
parents: 0
diff changeset
141 Diploid_2_AAGAGGCA_CGTCTAAT_R1fastqgz/chroms/length, Diploid_2_AAGAGGCA_CGTCTAAT_R1fastqgz/chroms/name,
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142 Diploid_2_AAGAGGCA_CGTCTAAT_R1fastqgz/indexes, Diploid_2_AAGAGGCA_CGTCTAAT_R1fastqgz/indexes/bin1_offset,
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143 Diploid_2_AAGAGGCA_CGTCTAAT_R1fastqgz/indexes/chrom_offset, Diploid_2_AAGAGGCA_CGTCTAAT_R1fastqgz/pixels,
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144 Diploid_2_AAGAGGCA_CGTCTAAT_R1fastqgz/pixels/bin1_id, Diploid_2_AAGAGGCA_CGTCTAAT_R1fastqgz/pixels/bin2_id,
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145 Diploid_2_AAGAGGCA_CGTCTAAT_R1fastqgz/pixels/count, Diploid_2_AAGAGGCA_TCTCTCCG_R1fastqgz,
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146 Diploid_2_AAGAGGCA_TCTCTCCG_R1fastqgz/bins, Diploid_2_AAGAGGCA_TCTCTCCG_R1fastqgz/bins/chrom,
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147 Diploid_2_AAGAGGCA_TCTCTCCG_R1fastqgz/bins/end, Diploid_2_AAGAGGCA_TCTCTCCG_R1fastqgz/bins/start,
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148 Diploid_2_AAGAGGCA_TCTCTCCG_R1fastqgz/chroms, Diploid_2_AAGAGGCA_TCTCTCCG_R1fastqgz/chroms/length,
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149 Diploid_2_AAGAGGCA_TCTCTCCG_R1fastqgz/chroms/name, Diploid_2_AAGAGGCA_TCTCTCCG_R1fastqgz/indexes,
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150 Diploid_2_AAGAGGCA_TCTCTCCG_R1fastqgz/indexes/bin1_offset, Diploid_2_AAGAGGCA_TCTCTCCG_R1fastqgz/indexes/chrom_offset,
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151 Diploid_2_AAGAGGCA_TCTCTCCG_R1fastqgz/pixels, Diploid_2_AAGAGGCA_TCTCTCCG_R1fastqgz/pixels/bin1_id,
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152 Diploid_2_AAGAGGCA_TCTCTCCG_R1fastqgz/pixels/bin2_id, Diploid_2_AAGAGGCA_TCTCTCCG_R1fastqgz/pixels/count'/></assert_contents>
0
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153 </output>
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154 </test>
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155 </tests>
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156 <help><![CDATA[
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157
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158 Quality control
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159 ===============
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160
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161 scHicQualityControl removes scHi-C interaction matrices with a too low read coverage or density. It creates four output files:
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162
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163 1. Read coverage plot
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164
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165 .. image:: $PATH_TO_IMAGES/read_coverage.png
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166
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167
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168 2. Density plot
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169
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170 .. image:: $PATH_TO_IMAGES/density.png
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171
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172 3. Quality report
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173
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174 .. code-block::
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175
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176 scHi-C sample contained 3882 cells:
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177 Number of removed matrices containing bad chromosomes 0
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178 Number of removed matrices due to low read coverage (< 100000): 1374
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179 Number of removed matrices due to too many zero bins (< 0.02 density, within 30000000 relative genomic distance): 610
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180 2508 samples passed the quality control. Please consider matrices with a low read coverage may be the matrices with a low density and overlap therefore.
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181
1
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182 4. The scHi-C scool matrix with the filtered matrices.
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183
0
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184 For more information about scHiCExplorer please consider our documentation on readthedocs.io_
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185
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186 .. _readthedocs.io: http://schicexplorer.readthedocs.io/
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187 ]]></help>
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188 <expand macro="citations" />
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189
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190 </tool>